Package picard.analysis
Class CompareMetrics
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.analysis.CompareMetrics
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@DocumentedFeature public class CompareMetrics extends CommandLineProgram
Compare two metrics files.
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Field Summary
Fields Modifier and Type Field Description boolean
IGNORE_HISTOGRAM_DIFFERENCES
List<File>
INPUT
List<String>
METRIC_ALLOWABLE_RELATIVE_CHANGE
List<String>
METRICS_TO_IGNORE
protected Map<String,Double>
MetricToAllowableRelativeChange
File
OUTPUT
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Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors Constructor Description CompareMetrics()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected picard.analysis.CompareMetrics.SimpleResult
compareMetricValues(Object value1, Object value2, String metricName)
protected String[]
customCommandLineValidation()
Put any custom command-line validation in an override of this method.protected int
doWork()
Do the work after command line has been parsed.-
Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Detail
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INPUT
@Argument(shortName="I", doc="Metric files to compare.", minElements=2, maxElements=2) public List<File> INPUT
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OUTPUT
@Argument(shortName="O", doc="Output file to write comparison results to.", optional=true) public File OUTPUT
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METRICS_TO_IGNORE
@Argument(shortName="MI", doc="Metrics to ignore. Any metrics specified here will be excluded from comparison by the tool.", optional=true) public List<String> METRICS_TO_IGNORE
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METRIC_ALLOWABLE_RELATIVE_CHANGE
@Argument(shortName="MARC", doc="Metric Allowable Relative Change. A colon separate pair of metric name and an absolute relative change. For any metric specified here, when the values are compared between the two files, the program will allow that much relative change between the two values.", optional=true) public List<String> METRIC_ALLOWABLE_RELATIVE_CHANGE
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IGNORE_HISTOGRAM_DIFFERENCES
@Argument(shortName="IHD", doc="Ignore any differences between the two metric file\'s histograms (useful if using the \'METRIC_ALLOWABLE_RELATIVE_CHANGE\')", optional=true) public boolean IGNORE_HISTOGRAM_DIFFERENCES
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Method Detail
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doWork
protected int doWork()
Description copied from class:CommandLineProgram
Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.- Specified by:
doWork
in classCommandLineProgram
- Returns:
- program exit status.
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customCommandLineValidation
protected String[] customCommandLineValidation()
Description copied from class:CommandLineProgram
Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.- Overrides:
customCommandLineValidation
in classCommandLineProgram
- Returns:
- null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.
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